(1) Background: Since fullerene C60 is insoluble in water and is toxic, it is not applicable in biomedicine and cosmetics. For this reason, the first derivative FD-C60 (fullerenol) was synthesized, which solved the problem of solubility in water and partially reduced toxicity. In order to maximally reduce toxicity and increase biomedical efficiency, the second derivative SD-C60 (3HFWC- Hyper-Harmonized-Hydroxylated Fullerene Water Complex), was created. (2) Methods: In order to obtain the most reliable data, several different methods are applicable in the characterization of FD-C60 and SD-C60 with water layers (NIR, FTIR, 13C-NMR, 1H-NMR, TGA/DTA, XRD, AFM/MFM etc.). (3) Results: FD-C60 as an individual structure is about 1.3 nm in size, while SD-C60 as an individual structure is 1030 nm in size. The aforementioned methods showed that SD-C60 contains water layers, which explains the difference between those two structures in the physicochemical properties, and their effects on biomolecules. (4) Conclusions: Based on the above methods and techniques, FD-C60 and SD-C60 are two different substances in terms of size, structure, and physicochemical properties; FD-C60 at 100C has endothermic characteristics and SD-C60 at 133C has exothermic characteristics, FD-C60 possesses water molecules only from humidity, while SD-C60 has water molecules from both humidity and extra water molecules in layers, the zeta potential of FD-C60 is -25.85 mV, while it is -43.29 mV for SD-C60.